Repeat comparison but include bombyx.
Compare to d melanogaster. then also comapre across in both directiosns.
Look for overlaps.
## Loading required package: magrittr
## Loading required package: tidyverse
## ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.0 ──
## ✔ ggplot2 3.3.2 ✔ purrr 0.3.4
## ✔ tibble 3.0.4 ✔ dplyr 1.0.2
## ✔ tidyr 1.1.2 ✔ stringr 1.4.0
## ✔ readr 1.4.0 ✔ forcats 0.5.0
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ tidyr::extract() masks magrittr::extract()
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag() masks stats::lag()
## ✖ purrr::set_names() masks magrittr::set_names()
## Loading required package: ShortRead
## Loading required package: BiocGenerics
## Loading required package: parallel
##
## Attaching package: 'BiocGenerics'
## The following objects are masked from 'package:parallel':
##
## clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
## clusterExport, clusterMap, parApply, parCapply, parLapply,
## parLapplyLB, parRapply, parSapply, parSapplyLB
## The following objects are masked from 'package:dplyr':
##
## combine, intersect, setdiff, union
## The following objects are masked from 'package:stats':
##
## IQR, mad, sd, var, xtabs
## The following objects are masked from 'package:base':
##
## anyDuplicated, append, as.data.frame, basename, cbind, colnames,
## dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
## grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
## order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
## rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
## union, unique, unsplit, which, which.max, which.min
## Loading required package: BiocParallel
## Loading required package: Biostrings
## Loading required package: S4Vectors
## Loading required package: stats4
##
## Attaching package: 'S4Vectors'
## The following objects are masked from 'package:dplyr':
##
## first, rename
## The following object is masked from 'package:tidyr':
##
## expand
## The following object is masked from 'package:base':
##
## expand.grid
## Loading required package: IRanges
##
## Attaching package: 'IRanges'
## The following objects are masked from 'package:dplyr':
##
## collapse, desc, slice
## The following object is masked from 'package:purrr':
##
## reduce
## Loading required package: XVector
##
## Attaching package: 'XVector'
## The following object is masked from 'package:purrr':
##
## compact
##
## Attaching package: 'Biostrings'
## The following object is masked from 'package:base':
##
## strsplit
## Loading required package: Rsamtools
## Loading required package: GenomeInfoDb
## Loading required package: GenomicRanges
## Loading required package: GenomicAlignments
## Loading required package: SummarizedExperiment
## Loading required package: Biobase
## Welcome to Bioconductor
##
## Vignettes contain introductory material; view with
## 'browseVignettes()'. To cite Bioconductor, see
## 'citation("Biobase")', and for packages 'citation("pkgname")'.
## Loading required package: DelayedArray
## Loading required package: matrixStats
##
## Attaching package: 'matrixStats'
## The following objects are masked from 'package:Biobase':
##
## anyMissing, rowMedians
## The following object is masked from 'package:dplyr':
##
## count
##
## Attaching package: 'DelayedArray'
## The following objects are masked from 'package:matrixStats':
##
## colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
## The following object is masked from 'package:purrr':
##
## simplify
## The following objects are masked from 'package:base':
##
## aperm, apply, rowsum
##
## Attaching package: 'GenomicAlignments'
## The following object is masked from 'package:dplyr':
##
## last
##
## Attaching package: 'ShortRead'
## The following object is masked from 'package:dplyr':
##
## id
## The following object is masked from 'package:purrr':
##
## compose
## The following object is masked from 'package:tibble':
##
## view
## The following object is masked from 'package:magrittr':
##
## functions
## Loading required package: Herper
## Loading required package: reticulate
file.copy("/rugpfs/fs0/brc/scratch/tcarroll/autoProcessing/BRC/obiroi/obiroi.fa", "obiroi.fa")
o_fa<-readFasta("obiroi.fa")
require(Herper)
export_CondaEnv("eggnog", yml_export= "eggnog_tom.yml", file.path("/rugpfs/fs0/brc/scratch/tcarroll/autoProcessing/","eggnogConda"))
import_CondaEnv("eggnog_tom.yml", "eggnog", pathToMiniConda="/rugpfs/fs0/brc/scratch/mpaul/herper_conda")
#install_CondaTools("ete3_external_apps","eggnog",pathToMiniConda="/rugpfs/fs0/brc/scratch/mpaul/herper/eggnog",updateEnv=TRUE,channels="etetoolkit",verbose=TRUE)
#external apps is not installed. this gives warning in build check. unclear why or if needed.
Herper::with_CondaEnv("eggnog",system("ete3 build check"),pathToMiniConda="/rugpfs/fs0/brc/scratch/mpaul/herper_conda")
Herper::with_CondaEnv("eggnog",system("ete3 ncbiquery -v 0"),pathToMiniConda="/rugpfs/fs0/brc/scratch/mpaul/herper_conda")
#install_CondaTools("python=2.7","eggnog",pathToMiniConda="/rugpfs/fs0/brc/scratch/mpaul/herper_conda",updateEnv=TRUE,channels="etetoolkit",verbose=TRUE)
#install_CondaTools("ete3_external_apps","eggnog",pathToMiniConda="/rugpfs/fs0/brc/scratch/mpaul/herper_conda",updateEnv=TRUE,channels="etetoolkit",verbose=TRUE)
# install_CondaTools(c("eggnog-mapper","ete3","ete_toolchain","ete3_external_apps"),"eggnog",channels="etetoolkit", pathToMiniConda= "/rugpfs/fs0/brc/scratch/mpaul/herper_conda/")
# install_CondaTools("ete3","eggnog",pathToMiniConda="/rugpfs/fs0/brc/scratch/mpaul/herper_conda",updateEnv=TRUE,channels="etetoolkit",verbose=TRUE)
# install_CondaTools("ete_toolchain","eggnog",pathToMiniConda="/rugpfs/fs0/brc/scratch/mpaul/herper_conda",updateEnv=TRUE,channels="etetoolkit",verbose=TRUE)
#install_CondaTools("ete3_external_apps","eggnog",pathToMiniConda="/rugpfs/fs0/brc/scratch/mpaul/herper/eggnog",updateEnv=TRUE,channels="etetoolkit",verbose=TRUE)read.delim("TC_ 20201201_Result/eggnogAnno_CondaVersionPy2_Scopeis50557_Targetis7227.emapper.annotations", skip = 3) %>% DT::datatable()## Warning in instance$preRenderHook(instance): It seems your data is too big
## for client-side DataTables. You may consider server-side processing: https://
## rstudio.github.io/DT/server.html